Mapping Heat Resistance in YeastsIn a proof-of-concept study, researchers demonstrated that a new genetic mapping strategy called RH-Seq can identify genes that promote heat resistance in the yeast Saccharomyces cerevisiae, allowing this species to grow better than its closest relative S. paradoxus at high temperatures.

First Monoploid Reference Sequence of SugarcaneFor the highly polyploid sugarcane, an international team of researchers has successfully assembled a first monoploid reference sequence using a targeted approach that focused on the gene rich part of the genome by harnessing information from a sequenced related species – sorghum.

Defining a Pan-Genome for Antarctic ArchaeaSome Antarctic lakes have salinities 10 times that of seawater. By collecting and sequencing dominant haloarchaeal sequences from six hypersaline lakes, researchers focused on understanding the genomic variation in haloarchaea across East Antarctica.

Methane Flux in the AmazonWetlands are the single largest global source of atmospheric methane. This project aims to integrate microbial and tree genetic characteristics to measure and understand methane emissions at the heart of the Amazon rainforest.

Insights into Functional Diversity in NeurosporaThis proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi.

Mining IMG/M for CRISPR-Associated ProteinsResearchers report the discovery of miniature CRISPR-associated proteins that can target single-stranded DNA. The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the JGI. The sequences were then biochemically characterized by a team led by Jennifer Doudna’s group at UC Berkeley.

DAS Tool for Genome Reconstruction from MetagenomesThrough the JGI’s Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. The work was published in Nature Microbiology.

Preparing for a Sequence Data DelugeThe approved CSP 2019 proposals leverage new capabilities and higher throughput in DNA sequencing, synthesis and metabolomics. Additionally, just over half of the accepted proposals come from primary investigators who have never led any previously accepted JGI proposal.

Innovative Technology Improves Our Understanding of Bacterial Cell SignalingCyclic di-GMP (Guanine Monophosphate) is found in nearly all types of bacteria and interacts with cell signaling networks that control many basic cellular functions. To better understand the dynamics of this molecule, researchers developed the first chemiluminescent biosensors for measuring cyclic di-GMP in bacteria through work enabled by the JGI’s Community Science Program (CSP).

Hidden Giants in Forest SoilsIn Nature Communications, giant virus genomes have been discovered for the first time in a forest soil ecosystem by JGI and University of Massachusetts-Amherst researchers. Most of the genomes were uncovered using a "mini-metagenomics" approach that reduced the complexity of the soil microbial communities sequenced and analyzed.

Symbiosis a Driver of Truffle DiversityTruffles are the fruiting bodies of the ectomycorrhizal (ECM) fungal symbionts residing on host plant roots. In Nature Ecology & Evolution, an international team sought insights into the ECM lifestyle of truffle-forming species. They conducted a comparative analysis of eight Pezizomycete fungi, including four species prized as delicacies.

Expanding Fungal Diversity, One Cell at a TimeIn Nature Microbiology, a team led by JGI researchers has developed a pipeline to generate genomes from single cells of uncultivated fungi. The approach was tested on several uncultivated fungal species representing early diverging fungi.

Project Management at JGI

JGI Project Managers work with users and JGI scientists and technical staff to prepare a Statement of Work (SOW) document that defines the scope of sequencing and analysis and lays out roles and responsibilities. The SOW includes the following items:

Platform and approximate quantity of JGI sequencing to address the scientific goals of the project, and timeline for the generation of this data, including responsibilities for analysis of early sample data to assess sequence for contamination, uniformity, and other quality control checks at the initial stages of the project. If contamination is a problem at this stage, the project may be suspended until suitable DNA is available.

Defined plan for maintaining regular communication between the JGI and collaborators through the duration of the project.

Defined responsibilities for collaborators and the JGI after the completion of sequencing, including genome assembly, automated and/or manual annotation, and other analyses, and initial plan for experimental and/or computational studies needed to address the specific scientific aims of the project.

The initial publication plan, including a provisional timeline and anticipated authorship. To the extent that JGI scientists contribute scientific and/or technical expertise or leadership to the project, it is expected that they will participate in the publication.

Acknowledgment of JGI Data Release policies, and affirmation that the project will conform to applicable safety regulations, including regulations that govern organisms that are pathogenic or could potentially be used as bioweapons.

Additionally, before sequencing of CSP projects can begin, users must sign a formal User Agreement that defines legal responsibilities of the JGI and the User.

Once a proposal has been approved through the review process, and the Statement of Work and User Agreement documents (if applicable) have been signed, the sequencing project may begin. Essential elements of the project are entered into JGI’s Integrated Tracking System (ITS) to allow staff to understand the requirements, history and status of any DOE JGI sequencing project. Active management of sequencing projects involves the following considerations:

Designation of a Project Manager within the JGI.

Designation of a principal collaborator or “Project Representative,” not necessarily the original applicant, who will be the JGI’s main point of contact throughout the duration of the sequencing project.

The collaborator must provide DNA or RNA, libraries, and other materials as described in the Statement of Work. Detailed guidelines for DNA/RNA submission are available. All materials described in the project proposal must be immediately available with the appropriate documentation and should be submitted to the JGI using the Collaborator Sample Information (CSI) form. Failure of the collaborator to provide materials described in the proposal in a timely fashion may lead to cancellation of the project and/or return of the proposal to the review panels.

Project components each require separate documentation. Those projects that are a composite of various components (whole-genome shotgun, cDNAs, BACs, etc.), will require separate documentation and sterility certificates (required for Risk Group 2 or higher organisms) for each component, or for resubmissions of a component (i.e. from new source materials to make a new library).

All source materials must pass the JGI QC process. Work will not commence on a new or resubmitted project component until the source material has passed the QC process.

The JGI’s Project Manager will communicate with the Project Representative to confirm, in a timely manner, when the initial sample data is of appropriate quality, free of contamination, etc.

Samples from approved projects will enter the production queue. This queue is managed primarily on a first-in/first-out basis, so it can take weeks or months for actual production to begin on a project, depending on the current workload and the length of time required to prepare and quality control representative libraries. Scheduling of the sequencing will be at the discretion of the JGI, given the overall production sequencing queue and the need to optimize available resources.

The post-sequencing analysis and publication plans must be coordinated and scheduled as specified in the Statement of Work.